Supersequences of Masks for Oligo-chips

@article{Gunoche2004SupersequencesOM,
  title={Supersequences of Masks for Oligo-chips},
  author={Alain Gu{\'e}noche},
  journal={Journal of bioinformatics and computational biology},
  year={2004},
  volume={2 3},
  pages={
          459-69
        }
}
  • A. Guénoche
  • Published 1 September 2004
  • Physics
  • Journal of bioinformatics and computational biology
On a very small surface, a chip, several thousands of oligonucleotides, can be synthesized using a mask technology. Given a set of oligos, the problems tackled here are: What is the minimum number of masks necessary to synthesize one copy of each oligo? How long will be the series of masks if each oligo is synthesized twice, such that the two copies are realized with two completely different series of masks? We establish that, for 20,000 oligos of 20 bases a single copy can be synthesized with… 

About the design of oligo-chips

An improved algorithm for the longest common subsequence problem

A hyper-heuristic for the Longest Common Subsequence problem

Chemical reaction optimization for solving longest common subsequence problem for multiple string

TLDR
The proposed chemical reaction optimization technique to solve the longest common subsequence problem for multiple instances for less execution time is compared with hyper-heuristic, ant colony optimization, beam ant colonies optimization, and memory-bound anytime algorithms.

A large neighborhood search heuristic for the longest common subsequence problem

TLDR
A large neighborhood search technique is presented that provides quality solutions to large k-LCSP instances and runs in linear time in both the length of the sequences and the number of sequences.

Probabilistic Beam Search for the Longest Common Subsequence Problem

TLDR
This work presents a probabilistic beam search approach to solve the longest common subsequence problem, and is believed to be the first stochastic local search algorithm proposed for this problem.

Longest common subsequence: an algorithmic component analysis

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and

Computing a longest common subsequence for multiple sequences

TLDR
A new nondeterministic algorithm based on stochastic and dynamic programming method inspired by the pheromone update strategy of the ant colony system is proposed for the longest common subsequence problem.

References

SHOWING 1-10 OF 10 REFERENCES

About the design of oligo-chips

The shortest common supersequence problem in a microarray production setting

TLDR
The results show that it is hard to beat ALPHABET-LEFTMOST in the microarray production setting by more than 2 characters, but these savings can improve overall oligo quality byMore than four percent.

The longest common subsequence problem revisited

This paper re-examines, in a unified framework, two classic approaches to the problem of finding a longest common subsequence (LCS) of two strings, and proposes faster implementations for both. Letl

The Shortest Common Supersequence Problem over Binary Alphabet is NP-Complete

The Complexity of Some Problems on Subsequences and Supersequences

TLDR
It is shown that theyes/no version of the LCS problem is NP-complete for sequences over an alphabet of size 2, and that the yes/no SCS problem isNPcomplete for sequence over an Alphabet of size 5.

On the Approximation of Shortest Common Supersequences and Longest Common Subsequences

Finding shortest common supersequences (SCS) and longest common subsequences (LCS) for a given set of sequences are two well-known NP-hard problems. They have important applications in many areas

On the Worst-Case Behaviour of Some Approximation Algorithms for the Shortest Common Supersequence of k Strings

Two natural polynomial-time approximation algorithms for the shortest common supersequence (SCS) of k strings are analysed from the point of view of worst-case performance guarantee. Both algorithms

Fidelity Probes for DNA Arrays

TLDR
A combinatorial approach is described which constructs a small set of fidelity probes that not only detect variations, but also point out the manufacturing step in which a variation has occurred.

Méthodes exacte et approchée pour leprobì eme de la plus longue sous-séquence communè a p chaˆchaˆınes de caractères

  • T.S.I
  • 1995